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    Comparative Genomic and Proteomic Analysis of SARS CoV-2 - with Potential Mutation Probabilities and Drug Targeting
    (2020) AKBULUT, EKREM
    COVID-19 caused by the highly pathogenic SARS-CoV-2 has caused the death of over 1.69 million people worldwide. High mutation potentials of RNA viruses require the determination of the most accurate structure to be targeted for treatment. In this study, comparative genomic and proteomic analyses of SARS-CoV-2 were performed using SARS-CoV and MERS-CoV, and the mutation potential of the residues was analyzed using bioinformatics tools. SARS-CoV-2 was found to be 80.08% and 58.79% similar to SARS-CoV and MERSCoV, respectively, at the nucleotide level. G+C content were 38%, 40.8% and 41.2% for SARS-CoV-2, SARS-CoV and MERS-CoV, respectively. 5?UTR G+C content was 44.6%, 43.5% and 44.7% for SARSCoV-2, MERS-CoV and SARS-CoV, respectively. At the amino acid level, SARS-CoV-2 and SARS-CoV showed 83.3% similarity, whereas SARS-CoV-2 and MERS-CoV showed 42.5% similarity. The E, M, N and S proteins of SARS-CoV-2 and SARS-CoV were found to be 94%, 90.1%, 90.6% and 76.1% identical, respectively. For SARS-CoV-2, 14 residues with a high risk of mutation and their repeat numbers in the genome were identified. Data from this study reveal that non-functional conserved proteins such as ORF6 and ORF7b with low risk of mutation may be appropriate targets for the treatment because of their functional properties.
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    Contribution of Polymorphism in PPAR? Untranslated Region to The Development of Axial Spondyloarthritis
    (2020) AKBULUT, EKREM; Ozgen, Metin
    The study aimed to contribute to the overall understanding of axial spondyloarthritis by investigating the polymorphism in 5’ untranslated region of peroxisome proliferator-activated receptor alpha gene in patients. The study included 194 patients and 197 controls recruited. The DNA obtained from the samples was genotyped by multiplex Polymerase Chain Reaction and then Matrix-Assisted Laser Desorption Ionization- Time of Flight Mass Spectrometry. Data were analyzed by logistic regression. Five polymorphic regions analyzed in this study, three of the sites were associated with disease risk. An allele in the rs1800204 polymorphic region (p < 0.001), C allele in the rs4253657 polymorphic region (p = 0.040) and C allele in the rs13909022 polymorphic region (p = 0.005) were associated with disease risk. The association of disease risk could not be detected with G and A alleles in the rs881740 (p = 0.456) and rs115640476 (p = 0.674) polymorphic regions, respectively. PPAR? 5' untranslated region polymorphism, which is shown to be associated with disease risk, is thought to contribute to the elucidation of the molecular mechanism of the disease. In axial spondyloarthritis, studying the effects of genetic changes in PPAR? on other genes with which it interacts will contribute to the full understanding of the molecular mechanism of the disease. Keywords: Axial spondyloarthritis; Peroxisome proliferator activated receptor alpha; Genetic predisposition; Disease risk.
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    Non-Structural Protein-13 Mutations in European Isolates of SARS-CoV-2 Changed Protein Stability
    (2024) ALHAN, Mehmet Emin; AKBULUT, EKREM
    Objective: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) became one of the most important health problems of the 21st century. Non-structural protein-13 (nsp13/helicase) plays an important role in the replication of the viral genome and the viral life cycle. The SARS-CoV-2 genome has undergone thousands of mutations since the disease first appeared. Mutations pose a threat to the validity of therapeutics due to changes in protein structure. Modeling alterations caused by mutations in the viral proteome contributes to the development of effective antivirals. The changes in protein structure and stability caused by mutations seen in European isolates of SARS-CoV-2 were analyzed in the study with the aim of contributing to studies on the development of new anti-virals and the validity of existing therapeutics. Methods: The changes in protein structure after mutation were modeled with deep learning algorithms. The alterations in protein stability were analyzed by SDM2, mCSM, DUET and DynaMut2. Results: The mutation analysis revealed four (Pro77Leu, Gly170Ser, Tyr324Cys, and Arg392Cys) missense mutations in the nsp13 protein in European isolates of SARS-CoV-2. Mutations caused changes in protein structure (rmsd 0.294 Å) and stability (-.58 ? ??G ? .003 kcal.mol-1). The atomic interactions formed by the mutant residues in the three-dimensional conformation of the protein have changed. Conclusion: The mutations seen in European isolates for nsp13 of SARS-CoV-2 may lead to the emergence of different phenotypes in terms of viral activity. For this reason, the study may contribute to the success of the fight against the virus with different treatment approaches in different regions.